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diff --git a/docs/dev/reference/mkinmod.html b/docs/dev/reference/mkinmod.html new file mode 100644 index 00000000..d26086eb --- /dev/null +++ b/docs/dev/reference/mkinmod.html @@ -0,0 +1,382 @@ +<!DOCTYPE html> +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Function to set up a kinetic model with one or more state variables — mkinmod • mkin</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link 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property="og:description" content="This function is usually called using a call to mkinsub() for each observed +variable, specifying the corresponding submodel as well as outgoing pathways +(see examples). +Print mkinmod objects in a way that the user finds his way to get to its +components."><meta name="robots" content="noindex"></head><body> + <a href="#main" class="visually-hidden-focusable">Skip to contents</a> + + + <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="default" aria-label="Site navigation"><div class="container"> + + <a class="navbar-brand me-2" href="../index.html">mkin</a> + + <small class="nav-text text-info me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">1.2.10</small> + + + <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> + <span class="navbar-toggler-icon"></span> + </button> + + <div id="navbar" class="collapse navbar-collapse ms-3"> + <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li> +<li class="nav-item dropdown"> + <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button> + <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/mkin.html">Introduction to mkin</a></li> + <li><hr class="dropdown-divider"></li> + <li><h6 class="dropdown-header" data-toc-skip>Example evaluations with (generalised) nonlinear least squares</h6></li> + <li><a class="dropdown-item" href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a></li> + <li><a class="dropdown-item" href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a></li> + <li><a class="dropdown-item" href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a></li> + <li><hr class="dropdown-divider"></li> + <li><h6 class="dropdown-header" data-toc-skip>Example evaluations with hierarchical models (nonlinear mixed-effects models)</h6></li> + <li><a class="dropdown-item" href="../articles/prebuilt/2022_dmta_parent.html">Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P</a></li> + <li><a class="dropdown-item" href="../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a></li> + <li><a class="dropdown-item" href="../articles/prebuilt/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a></li> + <li><a class="dropdown-item" href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a></li> + <li><a class="dropdown-item" href="../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a></li> + <li><a class="dropdown-item" href="../articles/web_only/multistart.html">Short demo of the multistart method</a></li> + <li><hr class="dropdown-divider"></li> + <li><h6 class="dropdown-header" data-toc-skip>Performance</h6></li> + <li><a class="dropdown-item" href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a></li> + <li><a class="dropdown-item" href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a></li> + <li><a class="dropdown-item" href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a></li> + <li><hr class="dropdown-divider"></li> + <li><h6 class="dropdown-header" data-toc-skip>Miscellaneous</h6></li> + <li><a class="dropdown-item" href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a></li> + <li><a class="dropdown-item" href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a></li> + </ul></li> +<li class="nav-item"><a class="nav-link" href="../coverage/coverage.html">Test coverage</a></li> +<li class="nav-item"><a class="nav-link" href="../news/index.html">News</a></li> + </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search"> + <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li> +<li class="nav-item"><a class="external-link nav-link" href="https://github.com/jranke/mkin/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li> + </ul></div> + + + </div> +</nav><div class="container template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + + <h1>Function to set up a kinetic model with one or more state variables</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/mkinmod.R" class="external-link"><code>R/mkinmod.R</code></a>, <a href="https://github.com/jranke/mkin/blob/HEAD/R/mkinsub.R" class="external-link"><code>R/mkinsub.R</code></a></small> + <div class="d-none name"><code>mkinmod.Rd</code></div> + </div> + + <div class="ref-description section level2"> + <p>This function is usually called using a call to <code>mkinsub()</code> for each observed +variable, specifying the corresponding submodel as well as outgoing pathways +(see examples).</p> +<p>Print mkinmod objects in a way that the user finds his way to get to its +components.</p> + </div> + + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">mkinmod</span><span class="op">(</span></span> +<span> <span class="va">...</span>,</span> +<span> use_of_ff <span class="op">=</span> <span class="st">"max"</span>,</span> +<span> name <span class="op">=</span> <span class="cn">NULL</span>,</span> +<span> speclist <span class="op">=</span> <span class="cn">NULL</span>,</span> +<span> quiet <span class="op">=</span> <span class="cn">FALSE</span>,</span> +<span> verbose <span class="op">=</span> <span class="cn">FALSE</span>,</span> +<span> dll_dir <span class="op">=</span> <span class="cn">NULL</span>,</span> +<span> unload <span class="op">=</span> <span class="cn">FALSE</span>,</span> +<span> overwrite <span class="op">=</span> <span class="cn">FALSE</span></span> +<span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for class 'mkinmod'</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span> +<span></span> +<span><span class="fu">mkinsub</span><span class="op">(</span><span class="va">submodel</span>, to <span class="op">=</span> <span class="cn">NULL</span>, sink <span class="op">=</span> <span class="cn">TRUE</span>, full_name <span class="op">=</span> <span class="cn">NA</span><span class="op">)</span></span></code></pre></div> + </div> + + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> + + +<dl><dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt> +<dd><p>For each observed variable, a list as obtained by <code>mkinsub()</code> +has to be specified as an argument (see examples). Currently, single +first order kinetics "SFO", indeterminate order rate equation kinetics +"IORE", or single first order with reversible binding "SFORB" are +implemented for all variables, while "FOMC", "DFOP", "HS" and "logistic" +can additionally be chosen for the first variable which is assumed to be +the source compartment. +Additionally, <code>mkinsub()</code> has an argument <code>to</code>, specifying names of +variables to which a transfer is to be assumed in the model. +If the argument <code>use_of_ff</code> is set to "min" +and the model for the compartment is "SFO" or "SFORB", an +additional <code>mkinsub()</code> argument can be <code>sink = FALSE</code>, effectively +fixing the flux to sink to zero. +In print.mkinmod, this argument is currently not used.</p></dd> + + +<dt id="arg-use-of-ff">use_of_ff<a class="anchor" aria-label="anchor" href="#arg-use-of-ff"></a></dt> +<dd><p>Specification of the use of formation fractions in the +model equations and, if applicable, the coefficient matrix. If "max", +formation fractions are always used (default). If "min", a minimum use of +formation fractions is made, i.e. each first-order pathway to a metabolite +has its own rate constant.</p></dd> + + +<dt id="arg-name">name<a class="anchor" aria-label="anchor" href="#arg-name"></a></dt> +<dd><p>A name for the model. Should be a valid R object name.</p></dd> + + +<dt id="arg-speclist">speclist<a class="anchor" aria-label="anchor" href="#arg-speclist"></a></dt> +<dd><p>The specification of the observed variables and their +submodel types and pathways can be given as a single list using this +argument. Default is NULL.</p></dd> + + +<dt id="arg-quiet">quiet<a class="anchor" aria-label="anchor" href="#arg-quiet"></a></dt> +<dd><p>Should messages be suppressed?</p></dd> + + +<dt id="arg-verbose">verbose<a class="anchor" aria-label="anchor" href="#arg-verbose"></a></dt> +<dd><p>If <code>TRUE</code>, passed to <code><a href="https://rdrr.io/pkg/inline/man/cfunction.html" class="external-link">inline::cfunction()</a></code> if +applicable to give detailed information about the C function being built.</p></dd> + + +<dt id="arg-dll-dir">dll_dir<a class="anchor" aria-label="anchor" href="#arg-dll-dir"></a></dt> +<dd><p>Directory where an DLL object, if generated internally by +<code><a href="https://rdrr.io/pkg/inline/man/cfunction.html" class="external-link">inline::cfunction()</a></code>, should be saved. The DLL will only be stored in a +permanent location for use in future sessions, if 'dll_dir' and 'name' +are specified. This is helpful if fit objects are cached e.g. by knitr, +as the cache remains functional across sessions if the DLL is stored in +a user defined location.</p></dd> + + +<dt id="arg-unload">unload<a class="anchor" aria-label="anchor" href="#arg-unload"></a></dt> +<dd><p>If a DLL from the target location in 'dll_dir' is already +loaded, should that be unloaded first?</p></dd> + + +<dt id="arg-overwrite">overwrite<a class="anchor" aria-label="anchor" href="#arg-overwrite"></a></dt> +<dd><p>If a file exists at the target DLL location in 'dll_dir', +should this be overwritten?</p></dd> + + +<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt> +<dd><p>An <code>mkinmod</code> object.</p></dd> + + +<dt id="arg-submodel">submodel<a class="anchor" aria-label="anchor" href="#arg-submodel"></a></dt> +<dd><p>Character vector of length one to specify the submodel type. +See <code>mkinmod</code> for the list of allowed submodel names.</p></dd> + + +<dt id="arg-to">to<a class="anchor" aria-label="anchor" href="#arg-to"></a></dt> +<dd><p>Vector of the names of the state variable to which a +transformation shall be included in the model.</p></dd> + + +<dt id="arg-sink">sink<a class="anchor" aria-label="anchor" href="#arg-sink"></a></dt> +<dd><p>Should a pathway to sink be included in the model in addition to +the pathways to other state variables?</p></dd> + + +<dt id="arg-full-name">full_name<a class="anchor" aria-label="anchor" href="#arg-full-name"></a></dt> +<dd><p>An optional name to be used e.g. for plotting fits +performed with the model. You can use non-ASCII characters here, but then +your R code will not be portable, <em>i.e.</em> may produce unintended plot +results on other operating systems or system configurations.</p></dd> + +</dl></div> + <div class="section level2"> + <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> + <p>A list of class <code>mkinmod</code> for use with <code><a href="mkinfit.html">mkinfit()</a></code>, +containing, among others,</p> +<dl><dt>diffs</dt> +<dd><p>A vector of string representations of differential equations, one for +each modelling variable.</p></dd> + +<dt>map</dt> +<dd><p>A list containing named character vectors for each observed variable, +specifying the modelling variables by which it is represented.</p></dd> + +<dt>use_of_ff</dt> +<dd><p>The content of <code>use_of_ff</code> is passed on in this list component.</p></dd> + +<dt>deg_func</dt> +<dd><p>If generated, a function containing the solution of the degradation +model.</p></dd> + +<dt>coefmat</dt> +<dd><p>The coefficient matrix, if the system of differential equations can be +represented by one.</p></dd> + +<dt>cf</dt> +<dd><p>If generated, a compiled function calculating the derivatives as +returned by cfunction.</p></dd> + + +</dl><p>A list for use with <code>mkinmod</code>.</p> + </div> + <div class="section level2"> + <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2> + <p>For the definition of model types and their parameters, the equations given +in the FOCUS and NAFTA guidance documents are used.</p> +<p>For kinetic models with more than one observed variable, a symbolic solution +of the system of differential equations is included in the resulting +mkinmod object in some cases, speeding up the solution.</p> +<p>If a C compiler is found by <code><a href="https://pkgbuild.r-lib.org/reference/has_compiler.html" class="external-link">pkgbuild::has_compiler()</a></code> and there +is more than one observed variable in the specification, C code is generated +for evaluating the differential equations, compiled using +<code><a href="https://rdrr.io/pkg/inline/man/cfunction.html" class="external-link">inline::cfunction()</a></code> and added to the resulting mkinmod object.</p> + </div> + <div class="section level2"> + <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h2> + <p>The IORE submodel is not well tested for metabolites. When using this +model for metabolites, you may want to read the note in the help +page to <a href="mkinfit.html">mkinfit</a>.</p> + </div> + <div class="section level2"> + <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2> + <p>FOCUS (2006) “Guidance Document on Estimating Persistence +and Degradation Kinetics from Environmental Fate Studies on Pesticides in +EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, +EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, +<a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics" class="external-link">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> +<p>NAFTA Technical Working Group on Pesticides (not dated) Guidance for +Evaluating and Calculating Degradation Kinetics in Environmental Media</p> + </div> + <div class="section level2"> + <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2> + <p>Johannes Ranke</p> + </div> + + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># Specify the SFO model (this is not needed any more, as we can now mkinfit("SFO", ...)</span></span></span> +<span class="r-in"><span><span class="va">SFO</span> <span class="op"><-</span> <span class="fu">mkinmod</span><span class="op">(</span>parent <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># One parent compound, one metabolite, both single first order</span></span></span> +<span class="r-in"><span><span class="va">SFO_SFO</span> <span class="op"><-</span> <span class="fu">mkinmod</span><span class="op">(</span></span></span> +<span class="r-in"><span> parent <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> m1 <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">SFO_SFO</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> <mkinmod> model generated with</span> +<span class="r-out co"><span class="r-pr">#></span> Use of formation fractions $use_of_ff: max </span> +<span class="r-out co"><span class="r-pr">#></span> Specification $spec:</span> +<span class="r-out co"><span class="r-pr">#></span> $parent</span> +<span class="r-out co"><span class="r-pr">#></span> $type: SFO; $to: m1; $sink: TRUE</span> +<span class="r-out co"><span class="r-pr">#></span> $m1</span> +<span class="r-out co"><span class="r-pr">#></span> $type: SFO; $sink: TRUE</span> +<span class="r-out co"><span class="r-pr">#></span> Coefficient matrix $coefmat available</span> +<span class="r-out co"><span class="r-pr">#></span> Compiled model $cf available</span> +<span class="r-out co"><span class="r-pr">#></span> Differential equations:</span> +<span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - k_parent * parent</span> +<span class="r-out co"><span class="r-pr">#></span> d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1</span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span> <span class="va">fit_sfo_sfo</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, solution_type <span class="op">=</span> <span class="st">"deSolve"</span><span class="op">)</span></span></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span> +<span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="co"># Now supplying compound names used for plotting, and write to user defined location</span></span></span> +<span class="r-in"><span> <span class="co"># We need to choose a path outside the session tempdir because this gets removed</span></span></span> +<span class="r-in"><span> <span class="va">DLL_dir</span> <span class="op"><-</span> <span class="st">"~/.local/share/mkin"</span></span></span> +<span class="r-in"><span> <span class="kw">if</span> <span class="op">(</span><span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/files2.html" class="external-link">dir.exists</a></span><span class="op">(</span><span class="va">DLL_dir</span><span class="op">)</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/r/base/files2.html" class="external-link">dir.create</a></span><span class="op">(</span><span class="va">DLL_dir</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="va">SFO_SFO.2</span> <span class="op"><-</span> <span class="fu">mkinmod</span><span class="op">(</span></span></span> +<span class="r-in"><span> parent <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span>, full_name <span class="op">=</span> <span class="st">"Test compound"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> m1 <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span>, full_name <span class="op">=</span> <span class="st">"Metabolite M1"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> name <span class="op">=</span> <span class="st">"SFO_SFO"</span>, dll_dir <span class="op">=</span> <span class="va">DLL_dir</span>, unload <span class="op">=</span> <span class="cn">TRUE</span>, overwrite <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> +<span class="r-msg co"><span class="r-pr">#></span> Copied DLL from /tmp/RtmpSeNGYy/file226312370605e2.so to /home/jranke/.local/share/mkin/SFO_SFO.so</span> +<span class="r-in"><span><span class="co"># Now we can save the model and restore it in a new session</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/readRDS.html" class="external-link">saveRDS</a></span><span class="op">(</span><span class="va">SFO_SFO.2</span>, file <span class="op">=</span> <span class="st">"~/SFO_SFO.rds"</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="co"># Terminate the R session here if you would like to check, and then do</span></span></span> +<span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://pkgdown.jrwb.de/mkin/">mkin</a></span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">SFO_SFO.3</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/readRDS.html" class="external-link">readRDS</a></span><span class="op">(</span><span class="st">"~/SFO_SFO.rds"</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">fit_sfo_sfo</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO.3</span>, <span class="va">FOCUS_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, solution_type <span class="op">=</span> <span class="st">"deSolve"</span><span class="op">)</span></span></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># Show details of creating the C function</span></span></span> +<span class="r-in"><span><span class="va">SFO_SFO</span> <span class="op"><-</span> <span class="fu">mkinmod</span><span class="op">(</span></span></span> +<span class="r-in"><span> parent <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> m1 <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>, verbose <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Program source:</span> +<span class="r-out co"><span class="r-pr">#></span> 1: #include <R.h></span> +<span class="r-out co"><span class="r-pr">#></span> 2: </span> +<span class="r-out co"><span class="r-pr">#></span> 3: </span> +<span class="r-out co"><span class="r-pr">#></span> 4: static double parms [3];</span> +<span class="r-out co"><span class="r-pr">#></span> 5: #define k_parent parms[0]</span> +<span class="r-out co"><span class="r-pr">#></span> 6: #define f_parent_to_m1 parms[1]</span> +<span class="r-out co"><span class="r-pr">#></span> 7: #define k_m1 parms[2]</span> +<span class="r-out co"><span class="r-pr">#></span> 8: </span> +<span class="r-out co"><span class="r-pr">#></span> 9: void initpar(void (* odeparms)(int *, double *)) {</span> +<span class="r-out co"><span class="r-pr">#></span> 10: int N = 3;</span> +<span class="r-out co"><span class="r-pr">#></span> 11: odeparms(&N, parms);</span> +<span class="r-out co"><span class="r-pr">#></span> 12: }</span> +<span class="r-out co"><span class="r-pr">#></span> 13: </span> +<span class="r-out co"><span class="r-pr">#></span> 14: </span> +<span class="r-out co"><span class="r-pr">#></span> 15: void diffs ( int * n, double * t, double * y, double * f, double * rpar, int * ipar ) {</span> +<span class="r-out co"><span class="r-pr">#></span> 16: </span> +<span class="r-out co"><span class="r-pr">#></span> 17: f[0] = - k_parent * y[0];</span> +<span class="r-out co"><span class="r-pr">#></span> 18: f[1] = + f_parent_to_m1 * k_parent * y[0] - k_m1 * y[1];</span> +<span class="r-out co"><span class="r-pr">#></span> 19: }</span> +<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># The symbolic solution which is available in this case is not</span></span></span> +<span class="r-in"><span><span class="co"># made for human reading but for speed of computation</span></span></span> +<span class="r-in"><span><span class="va">SFO_SFO</span><span class="op">$</span><span class="va">deg_func</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> function (observed, odeini, odeparms) </span> +<span class="r-out co"><span class="r-pr">#></span> {</span> +<span class="r-out co"><span class="r-pr">#></span> predicted <- numeric(0)</span> +<span class="r-out co"><span class="r-pr">#></span> with(as.list(odeparms), {</span> +<span class="r-out co"><span class="r-pr">#></span> t <- observed[observed$name == "parent", "time"]</span> +<span class="r-out co"><span class="r-pr">#></span> predicted <<- c(predicted, SFO.solution(t, odeini["parent"], </span> +<span class="r-out co"><span class="r-pr">#></span> k_parent))</span> +<span class="r-out co"><span class="r-pr">#></span> t <- observed[observed$name == "m1", "time"]</span> +<span class="r-out co"><span class="r-pr">#></span> predicted <<- c(predicted, (((k_m1 - k_parent) * odeini["m1"] - </span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 * k_parent * odeini["parent"]) * exp(-k_m1 * </span> +<span class="r-out co"><span class="r-pr">#></span> t) + f_parent_to_m1 * k_parent * odeini["parent"] * </span> +<span class="r-out co"><span class="r-pr">#></span> exp(-k_parent * t))/(k_m1 - k_parent))</span> +<span class="r-out co"><span class="r-pr">#></span> })</span> +<span class="r-out co"><span class="r-pr">#></span> return(predicted)</span> +<span class="r-out co"><span class="r-pr">#></span> }</span> +<span class="r-out co"><span class="r-pr">#></span> <environment: 0x5555577ec6d0></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># If we have several parallel metabolites</span></span></span> +<span class="r-in"><span><span class="co"># (compare tests/testthat/test_synthetic_data_for_UBA_2014.R)</span></span></span> +<span class="r-in"><span><span class="va">m_synth_DFOP_par</span> <span class="op"><-</span> <span class="fu">mkinmod</span><span class="op">(</span></span></span> +<span class="r-in"><span> parent <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"DFOP"</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"M1"</span>, <span class="st">"M2"</span><span class="op">)</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> M1 <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> M2 <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">fit_DFOP_par_c</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">m_synth_DFOP_par</span>,</span></span> +<span class="r-in"><span> <span class="va">synthetic_data_for_UBA_2014</span><span class="op">[[</span><span class="fl">12</span><span class="op">]</span><span class="op">]</span><span class="op">$</span><span class="va">data</span>,</span></span> +<span class="r-in"><span> quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="co"># }</span></span></span> +<span class="r-in"><span></span></span> +</code></pre></div> + </div> + </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2> + </nav></aside></div> + + + <footer><div class="pkgdown-footer-left"> + <p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown-footer-right"> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p> +</div> + + </footer></div> + + + + + + </body></html> + |